How to set the simularity threashold for treeplot

[cchd0001]

Hi dear developer,

First of all, thanks for creating this valuable tool, really appreciate it a lot.

Here is my issue: the similarity of the two classes is not too low (0.464371) but no link is displayed in the treeplot.
How can I reduce this similarity threshold to increase the links of treeplot ?

Best wishes,
Lidong Guo

[ChuanXu1]

@cchd0001, if two classes A and B are not matched, it is likely that one of them (for example, A) aligns with another cell type C which has a greater similarity compared to that between A and B. Otherwise, it is probable that these two cell types are not quite similar in the latent space (replacing the latent space with a better one such as that after batch correction will also yield optimal results sometimes). You can also adjust the parameter minimum_unique_percents in cellhint.harmonize to examine the outputs, as this will impact the threshold in cell type alignment.

[cchd0001]

Thanks.

In my case, A (from dataset_01) and B (from dataset_02) are matched if only this two dataset (dataset_01 and dataset_02) harmonize. Then I add dataset_03, A matched celltype C in dataset_03 but didn't match B any more.

BTW, the final order is dataset_02, dataset_01, dataset_03.

I will try this minimum_unique_percents.

Thanks again